Re: [Transdecoder-users] transdecoder output

[Brian H. <bh...@br...>]

Hi Dr. Jon,

The 'complete' designation indicates that both a start and stop codon are
found.  If it's 3' partial, then it's missing the 3' end (lacking a stop
codon).

There might be other competing methods, but I'm not sure what they are.
Others might comment here.

best,

~brian



On Mon, Aug 18, 2014 at 9:48 AM, Jon Lees <jon...@gm...> wrote:

> Dear Transdecoder Team
>
> I have started using transdecoder, and have an output peptide files.
>
> I was interested in understanding the header output
>
> for example what does type:3prime_partial compared to type:complete
>
> >CG43321-RA.A|m.2 CG43321-RA.A|g.2 type:3prime_partial len:122 gc:universal CG43321-RA.A:363-1(-)
> MHKFAPNSFGSPCRSSICAMVVILIIFRDIGRIKIKYFEELGQFLAHKSAQYNAGYNCDENSDVLVFIVLLSNFIYFFKVLEVVSTKWHFCVFISVTDFSVCSEMEYDIILIEISRLSPAK
> >CG43321.a|m.3 CG43321.a|g.3 type:3prime_partial len:103 gc:universal CG43321.a:306-1(-)
> MVVILIIFRDIGRIKIKYFEELGQFLAHKSAQYNAGYNCDENSDVLVFIVLLSNFIYFFKVLEVVSTKWHFCVFISVTDFSVCSEMEYDIILIEISRLSPAK
> >RluA-1.d|m.4 RluA-1.d|g.4 type:complete len:294 gc:universal RluA-1.d:292-1173(+)
> MEQQIRNRQVEKEYICRVEGVFPDGIVECKEPIEVVSYKIGVCKVSAKGKDCTTTFQKLSQNGTTSVVLCKPLTGRMHQIRVHLQYLGYPILNDPLYNHEVFGPLKGRSGDIGGKSDEELIRDLINIHNAENWLGIDCDSDISMFKSTKDEADRESLSSEHT
> SVVHHSDDDGCVNSRETTPPCNEPQQPENSVKLLETTNAVKEYQVAAQKSSSEICPAPLDAVESPLNGGGCNVGKVTVDEHCYECKVHYRDPKSKDLIMYLHAWKYKGPGWEYETELPNWARNDWDHLDSA*
>
> Are there any other methods that are competitive with transdecoder in terms of performance
>
> Thanks
>
> Dr Jon Lees
>
>
>
>
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-- 
--
Brian J. Haas
The Broad Institute
http://broad.mit.edu/~bhaas